Is MEGF8 p.Phe87= (c.261C>T) pathogenic?

MEGF8 p.Phe87= (c.261C>T) is classified Likely benign in MEGF8 (ClinVar, Single submitter, 1 submitter; last evaluated 2025-05-19). Very rare (popmax 0.00267%, afr); Associated with MEGF8-related Carpenter syndrome.

What condition is associated with MEGF8 p.Phe87= (c.261C>T)?

MEGF8 p.Phe87= (c.261C>T) is associated with MEGF8-related Carpenter syndrome (ClinVar).

How common is MEGF8 p.Phe87= (c.261C>T) in the general population?

MEGF8 p.Phe87= (c.261C>T) is very rare (popmax 0.00267%, afr) (gnomAD).

MEGF8 p.Phe87=

c.261C>T · rs370064427 · VCV2725796

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

very rare (popmax 0.00267%, afr)

Conditions

MEGF8-related Carpenter syndrome

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP -6.8
Overall
CADD	2.157	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.00267% African / African-American · 2/74,912 alleles

Filtering AF 0.000443% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.000166%

Overall 0.00062% 10/1,613,840 alleles · very rare exomes 7/1,461,660 · genomes 3/152,180 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	0.00267%	37,456
Finnishnot grpmax-eligible	0.00156%	63,986
South Asian	0.0011%	91,082
European (non-Finnish)	0.000509%	196,649

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: MEGF8
Protein: p.Phe87=
Coding: c.261C>T
MANE Select: NM_001271938
dbSNP: rs370064427
Type: single nucleotide variant
Location: chr19:42333678 (GRCh38)
Gene constraint: LOEUF 0.696 · pLI <0.01 (gnomAD)
Residue 87: the cub 1 domain

Full MEGF8 gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

MEGF8-related Carpenter syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

Similar variants

MEGF8 p.Arg419Ter Pathogenic/Likely pathogenic ★★ same condition
MEGF8 p.Arg991Ter Pathogenic/Likely pathogenic ★★ same condition
MEGF8 p.Ala1472Val Uncertain significance ★★ ⚠ same condition
MEGF8 p.Ala1572Thr Uncertain significance ★★ ⚠ same condition
MEGF8 p.Ala176Gly Uncertain significance ★★ ⚠ same condition
MEGF8 p.Ala1791Ser Uncertain significance ★★ same condition
MEGF8 p.Ala2104Ser Uncertain significance ★★ ⚠ same condition
MEGF8 p.Ala2349Gly Uncertain significance ★★ same condition

Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →

Cite Sugi Variant

Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/megf8-p-phe87 (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown